On denoising and compression of DNA microarray images

Baldi, 2002 Eisen, 1998, Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. USA, 95, 14863, 10.1073/pnas.95.25.14863 Spellman, 1998, Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization, Mol. Biol. Cell, 9, 3273, 10.1091/mbc.9.12.3273 Esteller, 2001, A gene hypermethylation profile of human cancer, Cancer Res., 61, 3225 Bassett, 1999, Gene expression informatics—its all in your mine, Nat. Genet. Suppl., 21, 51, 10.1038/4478 Brown, 2001, Image metrics in the statistical analysis of DNA microarray data, Proc. Natl. Acad. Sci., 98, 8944, 10.1073/pnas.161242998 Istepanian, 2003, Microarray image processing: current status and future directions, IEEE Trans. NanoBiosci., 2, 173, 10.1109/TNB.2003.816224 O’Neil, 2003, Improved processing of microarray data using image reconstruction techniques, IEEE Trans. NanoBiosci., 2, 176, 10.1109/TNB.2003.817022 Katzer, 2003, Methods for automatic microarray image segmentation, IEEE Trans. NanoBiosci., 2, 202, 10.1109/TNB.2003.817023 Microarrays: chipping away at the mysteries of science and medicine, http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html MacBeath, 2000, Printing proteins as microarrays for high-throughput function determination, Science, 289, 1760, 10.1126/science.289.5485.1760 Wang, 2003, Applications of wavelet modulus maxima in microarray spots recognition, IEEE Trans. NanoBiosci., 2, 190, 10.1109/TNB.2003.816230 Nagarajan, 2002, Identifying spots in microarray images, IEEE Trans. NanoBiosci., 1, 10.1109/TNB.2002.806936 Yang, 2002, Comparison of methods for image analysis on cDNA microarray data, J. Comput. Graph. Statist., 11, 108, 10.1198/106186002317375640 Wang, 2003, Microarray image enhancement by denoising using stationary wavelet transform, IEEE Trans. NanoBiosci., 2, 184, 10.1109/TNB.2003.816225 R. Jornsten, B. Yu, Comprestimation: microarray images in abundance, Proceedings, Conference on Information Science and Systems, Princeton University, March 15–17, 2000. Chang, 2000, Adaptive wavelet thresholding for image denoising and compression, IEEE Trans. Image Process., 9, 1532, 10.1109/83.862633 Lukac, 2004, A multichannel order-statistic technique for cDNA microarray image processing, IEEE Trans. NanoBiosci., 3, 272, 10.1109/TNB.2004.837907 Lukac, 2005, Vector filtering for color imaging, IEEE Signal Process., 22, 74, 10.1109/MSP.2005.1407717 Pitas, 1992, Order statistics in digital image processing, Proc. IEEE, 80, 1892, 10.1109/5.192071 Lukac, 2005, cDNA microarray image processing using fuzzy vector filtering framework, Fuzzy Sets and Systems, 152, 17, 10.1016/j.fss.2004.10.012 Donoho, 1995, De-noising by soft-thresholding, IEEE Trans. Inform. Theory, 41, 613, 10.1109/18.382009 Donoho, 1994, Ideal spatial adaptation via wavelet shrinkage, Biometrika, 81, 425, 10.1093/biomet/81.3.425 R. Jornsten, W. Wang, B. Yu, K. Ramchandran. Microarray image compression: SLOCO and the effects of information loss, Signal Process. J. (Special issue on genomic signal processing) (2002). Weinberger, 2000, The LOCO-I lossless image compression algorithm: principles and standardization into JPEG-LS, IEEE Trans. Image Process., 9, 10.1109/83.855427 Faramarzpour, 2003, Lossless DNA microarray image compression, IEEE Conf. Signal Systems Comput., 2, 1501 N. Faramazpour, S. Shirani, Lossless and lossy compression of DNA microarray image, Proceedings, IEEE Data Compression Conference (DCC ‘04’), 2004. J. Hua, Z. Liu, Z. Xiong, Q. Wu, K. Castleman, Microarray BASICA: Background adjustment, segmentation, image compression and analysis of microarray images, Proceedings of the International Conference on Image Processing, vol. 1, 2003. S. Lonardi, Y. Luo, Gridding and compression of microarray images, Proceedings, 2004 IEEE Computational Systems Bioinformatics Conference (CSB 2004), 2004. Samavi, 2003, DNA microarray image compression by pipeline architecture, Proc. IEEE Conf. Signal Systems Comput., 2, 2176 Schuchhardt, 2000, Normalization strategies for cDNA microarrays, Nucl. Acids Res., 28, 10.1093/nar/28.10.e47 D. Kundu, M.Z. Raqab, Generalized Rayleigh distribution: different methods of estimation, http://home.iitk.ac.in/∼kundu/pap.html. Coifman, 1995, Translation-invariant denoising Lang, 1996, Noise reduction using an undecimated discrete wavelet transform, IEEE Signal Process. Lett., 3, 10, 10.1109/97.475823 Wu, 1997, Context-based, adaptive, lossless image coding, IEEE Trans. Commun., 45, 437, 10.1109/26.585919 Y. Zhang, D. Adjeroh, Prediction by partial approximate matching for lossless image compression, Proceedings, IEEE Data Compression Conference, Snowbird, Utah, March 2005, p. 494. Cleary, 1997, Unbounded length contexts for PPM, Comput. J., 40, 67, 10.1093/comjnl/40.2_and_3.67 R. Jornsten, Y. Vardi, C.-H. Zhang, On the bit-plane compression of microarray images, http://www.stat.rutgers.edu/∼rebecka/ Yeung, 2003, Clustering gene-expression data with repeated measurements, Genome Biol., 4, R34, 10.1186/gb-2003-4-5-r34 He, 2002, On quantitative evaluation of clustering systems